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  <div class="section" id="topology-modules">
<h1>4. Topology modules<a class="headerlink" href="#topology-modules" title="Permalink to this headline">¶</a></h1>
<p>The topology module contains the functions to read topology
files. MDAnalysis uses topology files to identify atoms and bonds
between the atoms. It can use topology files from MD packages such as
CHARMM&#8217;s and NAMD&#8217;s PSF format or Amber&#8217;s PRMTOP files. In addition,
it can also glean atom information from single frame coordinate files
such the PDB, CRD, or PQR formats.</p>
<p>Typically, MDAnalysis recognizes formats by the file extension
and hence most users probably do not need to concern themselves with
classes and functions described here.</p>
<p class="rubric">Contents</p>
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<ul>
<li class="toctree-l1"><a class="reference internal" href="topology/init.html">4.1. Topology readers &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.topology</span></tt></a></li>
<li class="toctree-l1"><a class="reference internal" href="topology/core.html">4.2. Common functions for topology building &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.topology.core</span></tt></a></li>
<li class="toctree-l1"><a class="reference internal" href="topology/tables.html">4.3. MDAnalysis topology tables</a></li>
<li class="toctree-l1"><a class="reference internal" href="topology/PSFParser.html">4.4. PSF topology parser</a></li>
<li class="toctree-l1"><a class="reference internal" href="topology/TOPParser.html">4.5. Amber PRMTOP topology parser</a></li>
<li class="toctree-l1"><a class="reference internal" href="topology/CRDParser.html">4.6. CRD topology parser</a></li>
<li class="toctree-l1"><a class="reference internal" href="topology/GROParser.html">4.7. GRO topology parser</a></li>
<li class="toctree-l1"><a class="reference internal" href="topology/PDBParser.html">4.8. PDB topology parser</a></li>
<li class="toctree-l1"><a class="reference internal" href="topology/PrimitivePDBParser.html">4.9. Primitive PDB topology parser</a></li>
<li class="toctree-l1"><a class="reference internal" href="topology/PDBQTParser.html">4.10. PDBQT topology parser</a></li>
<li class="toctree-l1"><a class="reference internal" href="topology/PQRParser.html">4.11. PQR topology parser</a></li>
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